Statistical methods for the discovery of co-operative transcription factors: co-bind code revised

Discovering co-operative transcription factors (TF's) within the genome is a computationally challenging problem, tackled through Monte Carlo-like analysis by the Co-Bind code, developed at the Department of Genetics of the St. Louis Washington University. Due to its statistical nature, co-bind is characterized by very long execution times, order of days on current high-end workstations, and could benefit from parallelization and a wise optimization, performed at both the algorithmic and coding levels. This paper presents the results achieved by parallelizing co-bind and optimising the parallel code and shows that, on a 16-processor architecture, a speedup greater than two orders of magnitude is achieved with respect to the serial version released by the code's authors.